I’ve read through the Sovrin Whitepaper and a couple of other materials I was able to find, and after finishing it, a couple of questions remain.

Most importantly: The idea to use decentralized and pseudonymous IDs seems to be realizable using any (public) distributed ledger. Why is Sovrin built on top of Indy, rather than remaining Ledger-Agnostic?

And related to this, what exactly is the advantage for Sovrin to be a permissioned chain, rather than a permissionless chain?

From the identity-perspective, building a permission-based system on top of a permissionless system is very easy, so I can only conclude that it is done to have some regulatory saying in who starts running a node. Maybe this is done to be able to use a faster consensus mechanism than the large-scale-permissionless-BFT-Consensus-algorithms we know so far, but it feels like still putting my trust into the hands of a couple of large organizations+companies, rather than not needing any trust because I can interface with the system directly.

The idea to use decentralized and pseudonymous IDs seems to be realizable using any (public) distributed ledger. Why is Sovrin built on top of Indy, rather than remaining Ledger-Agnostic?

The Sovrin network is has been built for a singular purpose, identity creation, management, and verification. Being purpose-built, the network is allowed to be optimized and managed in a more effective way.

What exactly is the advantage for Sovrin to be a permissioned chain, rather than a permissionless chain?

This is done for trust and speed. The Sovrin Foundation can help administer a more trustworthy network using the trust framework, and the network is much more efficient when only a small pool of nodes are needed to push changes to the ledger.

Keep in mind however, that reading from the ledger is public/permissionless.